Summary: Translating genome sequence information into functional information is a grand challenge in basic and applied biomedicine. Results from many large-scale programs designed to annotate the human genome have led to the discovery that many novel proteins and protein forms exist in the proteome. Determining how and when such proteins are made is essential to understanding the magnitude of our expanded proteome. One possibility is that novel proteins are a product of translation events mediated by internal ribosomal entry sites (IRESs). For example, many cellular IRESs associate with genes whose products are responsible for controlling cell growth and death. Whether IRES-mediated translation is more prevalent than previously thought is a matter of opinion, but some speculate that up to 10% of all RNA transcripts have IRESs imbedded in their sequences. This notion is supported by the discovery that IRES-mediated translation is responsible for making the MPD6 protein in the humoral immune response. Unfortunately, scientific progress in this area has been limited by our inability to identify IRES signatures at the DNA level. Here we propose to develop a genome-wide approach to finding motifs that behave as IRESs and examine their preponderance in the human genome. An integrated experimental-bioinformatics approach will be employed to validate these putative IRESs. Results from this study will illuminate the extent and nature of the proteome that is encoded by a well-established, non-classical translational mechanism. Because IRES-mediated translation is known to occur in cells under stress and in altered conditions, our results will be invaluable to understanding protein expression in disease states. By developing a more global view of the human genome and the genes encoded in these sequences, it should be possible to realize how defects in the genome manifest themselves in specific disease forms. It is expected that such knowledge will lead to new therapeutic interventions that can be used to improve the human condition.